package mBio;

import java.io.*;
import java.util.*;
import rfBio.*;

public class remove_fasta {

	public static void main(String[] args)
	 throws IOException, FileNotFoundException{
		
		Bioutil test = new Bioutil();

		if(args.length != 4){
			System.out.println("Wrong number of parameters!" + '\n' + "Usage: remove_fasta infile list outfile type.");
			System.exit(0);
			
		}

		if( (args[3].equals("p")) || (args[3].equals("P")) || (args[3].equals("d")) || (args[3].equals("D")) || (args[3].equals("r")) || (args[3].equals("R")) ){
			// type OK
		}
		else{
			System.out.println("Invalide type. as to be either p,d or r");
			System.exit(0);
		}
		fasta f = new fasta(args[0], args[1]);
		
		if( (args[3] == "p") || (args[3] == "P")){
			f.set_type("p");
		}
		if( (args[3] == "d") || (args[3] == "D")){
			f.set_type("d");
		}
		if( (args[3] == "r") || (args[3] == "R")){
			f.set_type("r");
		}
		f.clean();
		f.writeFasta(args[2]);
		
	}

}
